Allows gene set over-representation analysis (ORA). LEGO takes a network-based approach to transform the functional non-equivalence roles of genes and gene-gene interactions into gene weights, and then incorporates the weights in ORA analysis. The software can be useful for identifying functionally relevant gene sets and deriving novel hypothesis in functional genomics studies, and for large-scale functional genomics studies. It was applied to two lists of autism-related genes identified by recent large-scale whole exome sequencing studies and discovered relevant gene sets to autism.

State Key Laboratory of Genetic Engineering, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai, China; Children’s Hospital of Fudan University, Shanghai, China

LEGO funding source(s)

Supported by National Basic Research Program of China [2012CB316505, 2010CB529505]; the National Natural Science Foundation of China [30971643, 31071113, 91231116]; the Specialized Research Fund for the Doctoral Program of Higher Education of China [20120071110018]; the Innovation Program of Shanghai Municipal Education Commission [13ZZ006]; the National Institutes of Health (grant D43TW007887).